> I wonder what part of "a perpetual license to develop and market
> AmigaOS 4" they find unclear.

The first controversial wording, relating to object code and source code use, is this (emphasis mine):

"the Amiga Parties hereby grant Hyperion [...] an exclusive, perpetual, worldwide and royalty-free, transferable right and Object Code and Source Code license to the Software in order to use, develop, modify, commercialize, distribute and market the Software in any form (including through sublicensing), on any medium [...], through any means (including but not limited to making AmigaOS 4 available to the public via the internet) and for any current or future hardware platform."

...with "the Software" meaning Commodore's AmigaOS 3.1 in *both* occurences, of course. One might suspect that the second occurence was actually meant to say "AmigaOS 4" instead of "the Software" (as it does in Hyperion's subsequent press release). But that's not what it says in the settlement agreement. And even if it did, see below.

The second controversial wording, relating to your quote about trademark use, is this (emphasis mine):

""AmigaOS 4" means the Operating System developed by Hyperion and based in part on the Software, including without limitation the Software Architecture of the Software as described in the Documentation, in any version (irrespective of version numbering, e.g., AmigaOS 5)."

Hyperion claim that this definition of "AmigaOS 4" also applies to what they released as AmigaOS 3.1.4.